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"fin_ac": fields[170],
"fin_af": fields[171],
"nfe_ac": fields[172],
"nfe_af": fields[173]
},
"clinvar": {
"rs": fields[176],
"clinsig": fields[177],
"trait": fields[178],
"golden_stars": fields[179]
},
"gtex": gtex
}
}
one_snp_json = list_split(dict_sweep(unlist(value_convert_to_number(one_snp_json)), vals=["."]), ";")
one_snp_json["dbnsfp"]["chrom"] = str(one_snp_json["dbnsfp"]["chrom"])
return one_snp_json
"hgvs": [i for i in df["clinvar_hgvs"].split("|") if i != "."],
"omim": [i for i in df["clinvar_OMIM_id"].split("|") if i != "."],
"medgen": [i for i in df["clinvar_MedGen_id"].split("|") if i != "."],
"orphanet": [i for i in df["clinvar_Orphanet_id"].split("|") if i != "."],
"var_source": [i for i in df["clinvar_var_source"].split("|") if i != "."]
},
"hgvsc": list(set(df["HGVSc_ANNOVAR"].split(';') + df["HGVSc_snpEff"].split(';') + df["HGVSc_VEP"].split(';'))),
"hgvsp": list(set(df["HGVSp_ANNOVAR"].split(';') + df["HGVSp_snpEff"].split(';') + df["HGVSp_VEP"].split(';'))),
"gtex": list(gtex),
"geuvadis_eqtl_target_gene": df["Geuvadis_eQTL_target_gene"]
}
}
if include_gnomad:
one_snp_json['dbnsfp'].update(gnomad)
one_snp_json = list_split(dict_sweep(unlist(value_convert_to_number(one_snp_json)), vals=[".", '-', "NA", None], remove_invalid_list=True), ";")
one_snp_json["dbnsfp"]["chrom"] = str(one_snp_json["dbnsfp"]["chrom"])
return one_snp_json
"fin_ac": fields[122],
"fin_af": fields[123],
"nfe_ac": fields[124],
"nfe_af": fields[125],
"sas_ac": fields[126],
"sas_af": fields[127]
},
"clinvar": {
"rs": fields[128],
"clinsig": fields[129],
"trait": fields[130]
}
}
}
one_snp_json = list_split(dict_sweep(unlist(value_convert_to_number(one_snp_json)), vals=["."]), ";")
one_snp_json["dbnsfp"]["chrom"] = str(one_snp_json["dbnsfp"]["chrom"])
return one_snp_json
try:
if doc["vartype"] != "snv":
ref = "T" + doc["ref"]
alt = "T" + doc["alt"]
else:
ref = doc["ref"]
alt = doc["alt"]
if doc["vartype"] in ["ins", "del", "delins"]:
doc[assembly]['start'], doc[assembly]['end'] = get_pos_start_end(doc["chrom"], pos - 1, ref, alt)
else:
doc[assembly]['start'], doc[assembly]['end'] = get_pos_start_end(doc["chrom"], pos, ref, alt)
except (ValueError, AssertionError):
doc[assembly] = {}
if hgvs:
doc["_id"] = hgvs.replace('chr23', 'chrX').replace('chr24', 'chrY')
yield dict_sweep(unlist(value_convert_to_number(doc, skipped_keys=['chrom', 'ref', 'alt', 'allele', 'deleted_sequence', 'inserted_sequence'])), vals=[[], {}, None])
ref = item.REF
info = item.INFO
hpo_count=item.INFO['HPO_CT']
for alt in item.ALT:
alt = str(alt)
(HGVS, var_type) = get_hgvs_from_vcf(chrom, chromStart, ref, alt, mutant_type=True)
if HGVS is None:
return
one_snp_json = {
"_id": HGVS,
"geno2mp": {
"hpo_count": hpo_count,
}
}
obj = (dict_sweep(unlist(value_convert_to_number(one_snp_json)), [None]))
yield obj
for _start in key_start:
one_snp_json['gnomad_genome'][_start.lower()] = {}
# loop through each available key
for _key in keys:
if _key in info:
# loop through each prefix
for _start in key_start_new:
# "ac", "af" value is related to multi-allelic, need to deal with separately
if _key.startswith(_start):
if _start == 'nhomalt':
one_snp_json['gnomad_genome']['hom'][_key.replace('nhomalt', 'hom')] = info[_key][i]
elif _start in ['AC', 'AF', 'Hemi']:
one_snp_json['gnomad_genome'][_start.lower()][_key.lower()] = info[_key][i]
else:
one_snp_json['gnomad_genome'][_start.lower()][_key.lower()] = info[_key]
obj = (dict_sweep(unlist(value_convert_to_number(one_snp_json, skipped_keys=['chrom'])), [None]))
yield obj
"hom_sas": info['Hom_SAS']
},
"inbreedingcoeff": inbreedingcoeff,
"mq": {
"mq": info['MQ'],
"mq0": info['MQ0'],
"mqranksum": mqranksum
},
"ncc": info['NCC'],
"qd": qd,
"readposranksum": readposranksum,
"vqslod": info['VQSLOD'],
"culprit": info['culprit']
}
}
obj = (dict_sweep(unlist(value_convert_to_number(one_snp_json)), [None]))
yield obj
for _start in key_start:
one_snp_json['gnomad_exome'][_start.lower()] = {}
# loop through each available key
for _key in keys:
if _key in info:
# loop through each prefix
for _start in key_start_new:
# "ac", "af" value is related to multi-allelic, need to deal with separately
if _key.startswith(_start):
if _start == 'nhomalt':
one_snp_json['gnomad_exome']['hom'][_key.replace('nhomalt', 'hom')] = info[_key][i]
elif _start in ['AC', 'AF', 'Hemi']:
one_snp_json['gnomad_exome'][_start.lower()][_key.lower()] = info[_key][i]
else:
one_snp_json['gnomad_exome'][_start.lower()][_key.lower()] = info[_key]
obj = (dict_sweep(unlist(value_convert_to_number(one_snp_json, skipped_keys=['chrom'])), [None]))
yield obj
"hom_sas": info['Hom_SAS']
},
"inbreedingcoeff": inbreedingcoeff,
"mq": {
"mq": info['MQ'],
"mq0": info['MQ0'],
"mqranksum": mqranksum
},
"ncc": info['NCC'],
"qd": qd,
"readposranksum": readposranksum,
"vqslod": info['VQSLOD'],
"culprit": info['culprit']
}
}
obj = (dict_sweep(unlist(value_convert_to_number(one_snp_json)), [None]))
yield obj